Heparin-like glycosaminoglycans (HLGAGs) are key components of the extracellular matrix (ECM) that serve to regulate an array of biological functions (Jackson, R. L., Busch, S. J., Cardin, A. D. (1991) Physiological Reviews 71, 481-539; Lindahl, U., Lidhold, K., Spillman, D., Kjellén, L. (1994) Thrombosis Research 75, 1-32). HLGAGs, which include the polysaccharides heparin and heparan sulfate, are characterized by a disaccharide repeating unit of uronic acid and hexosomaine, where the uronic acid is either L-iduronic acid or D-glucuronic acid and the hexosamine is linked to the uronic acid by a 1-4 linkage (Jackson, R. L., Busch, S. J., & Cardin, A. D. (1991) Physiol. Rev. 71:481-539). Heparin possesses predominantly L-iduronic acid with a high degree of sulfation (Conrad, H. E. (1989) Ann. N.Y. Acad. Sci. 556, 18-28; Ernst, S., Langer, R., Cooney, C. L., Sasisekharan, R. (1995) CRC Critical Rev. Biochem. Mol. Biol. 30, 387-444). Heparan sulfate is chemically similar to heparin but contains less 2-O-sulfate and N-sulfate groups than heparin and also possesses a higher percentage of D-glucuronic acid within the polymer (Conrad, H. E. (1989) Ann. N.Y. Acad. Sci. 556, 18-28; Lindhardt, R. J., Rice, K. G., Kim, Y. S., Lohse, D. L., Wang, H. M., Loganathan, D. (1988) Biochem. J. 254, 781-87). HLGAGs are complex due to the high degree and varying patterns of sulfation and acetylation on both the uronic acid and the hexosamine residues. It is believed that it is the sulfation which is responsible for the numerous different functional roles of these carbohydrates.
Our understanding of heparin's and heparan-sulfate's functional role is severely limited, however, by our limited knowledge of the heparin and heparan sulfate sequence. In fact one of the major challenges in elucidating a specific role for HLGAGs in certain biological systems is that the considerable chemical heterogeneity of HLGAGs has thwarted attempts to determine sequence-function relationships (Ernst, S., Langer, R., Cooney, C. L., Sasisekharan, R. (1995) CRC Critical Rev. Biochem. Mol. Biol. 30, 387-444; Hascall, V. C., Midura, R. J. (1989) in Keratan Sulphate—Chemistry, Biology, Clinical Pathology (Greilling, H. and Scott, J. E., eds.), pp. 66-73, The Biochemical Society, London).
HLGAG degrading enzymes, or heparinases, are a family of polysaccharide lyases that catalyze the cleavage of HLGAGs through an elimination reaction by a nucleophilic amino acid. Heparinases have proved to be useful tools in heparin degradation and in providing composition and sequences information (Linhardt, R. J., Turnbull, J. E., Wang, H. M., Longanathan, D., & Gallagher, J. T. (1990) Biochemistry 29:2611-2617). F. haparinum produces at least three types of haparinases (I, II and III) with different substrate specificities (Lohse, D. L., & Linhardt, R. J. (1992) J. Biol. Chem. 267:24347-24355). All three enzymes have been cloned and recombinantly expressed (Sasisekharan, R., Bulmer, M., Moremen, K. W., Cooney, C. L., Langer, R. (1993) Proc. Natl. Acad. Sci. USA 90, 3660-64; Godavarti, R., Davis, M., Venkataraman, G., Cooney, C, Langer, R, and Sasisekharan, R (1996a) Biochem. Biophys. Res. Comm. 225, 751-758; Godavarti, R., Cooney, Cl. L., Lnager, R., Sasisekharan, R. (1996b) Biochemistry 35, 6846-6852; Ernst, S., Venkataraman, G., Winkler, S., Godavarti, R., Langer, R., Cooney, C. L., Sasisekharan, R. (1996) Biochem. J. 315, 589-597).
The three heparinases, from F. heparinum, are distinguished on the basis of their size, charge properties, and substrate specificities (Ernst, S., Langer, R., Cooney, C. L., Sasisekharan, R. (1995) CRC Critical Rev. Biochem. Mol. Biol. 30, 387-444). Heparinase I, a 42 kDa protein with a pI of 8.5-9.3, primarily cleaves HLGAGs at sites with an O-sulfated-L-iduronic acid linkage (i.e., heparin-like regions). Heparinases III, a 73 kDa protein with a pI of about 9, requires primarily an unsulfated D-glucuronic acid moiety (heparan sulfate-like regions). While there is evidence for a secondary substrate specificity for heparinases I and III (Yamada, S., Mukarkami, T. Tsuda, H., Yoshida, K. Sugahara, K. (1995) J. Biol. Chem. 270, 8696-705; Desai, U., Wang, H., Linghardt, R. (1993) Arch. Biochem. Biophys. 306, 461-8), these enzymes do show a predominant enzymatic preference for a C5 epimer of uronic acid, with heparinase III primarily acting at hexosamine-glucuronic acid linkages and heparinase I acting primarily at hexosamine-iduronic acid linkages. Heparinase II is the largest of the heparinases and has the broadest substrate specificity. The 84 kDa protein has a pI of around 9 and cleaves both heparin and heparan sulfate-like regions of HLGAGs (Ernst, S., Lnager, R., Cooney, C. L., Sasisekharan, R. (1995) CRC Critical Rev. Biochem. Mol. Biol. 30, 387-444; Lohse, D. L., Linhardt, R. J. (1992) J. Biol. Chem. 267, 24347-55). Thus, unlike heparinase I and heparinase III, which distinguish between the C5 epimers L-iduronic acid and D-glucuronic acid, heparinase II is catalytically active towards both (Ernst, S., Langer, R., Cooney, C. L., Saisekharan, R. (1995) CRC Critical Rev. Biochem. Mol. Biol. 30, 387-444).
Through extensive biochemical and site-directed mutagenesis experiments, our studies with heparinase I have led to the identification of three residues: cysteine 135, histidine 203, and lysine 199, that are critical for enzymatic function (Godavarti, R., Cooney, C. L. Langer, R., Sasisekharan, R. (1996b) Biochemistry 35, 6846-6852; Ernst, S. , Venkataraman, G., Winkler, S., Godavarti, R., Lnager, R., Cooney, C. L., Sasisekharan, R. (1996) Biochem. J. 315, 589-597; Sasisekharan, R., Leckband, D., Godavarti, R., Venkataraman, G., Cooney, C. L., Lnager, R. (1995) Biochemistry 34, 14441-14448, and PCT Patent Application WO 97/16556, claiming priority to U.S. Provisional patent application Ser. No. 60/008,069, and it's related U.S. National Phase patent application. (Ser. No. 09/066,481), which is hereby incorporated by reference). A mechanism was proposed wherein cysteine 135 was the active site-base that abstracted the C5 hydrogen from iduronic acid, which, when coupled to the cleavage of the glycosidic bond, led to the formation of the 4.5-unsaturated uronate product (Sasisekharan, R., Leckband, D., Godavarti, R., Venkataraman, G., Cooney, C. L., Lnager, R. (1995) Biochemistry 34, 14441-14448). Thus, a stereospecific role for cysteine 135 was posited that allowed heparinas I to distinguish between heparin and heparan sulfate-like regions.
It is desirable to develop molecular tools that can serve to elucidate structure-function relationships between HLGAGs and biological molecules, such as growth factors and cytokines. One such tool has proved to be the three heparinases derived from F. heparinum (Linhardt, R. J., et al., Heparin and Related Polysaccharides, (Lane, D. A., et al eds.) P. 37-47, Plenum Press, New York). Using heparinases, HLGAGs have been show to be critical players in major biological functions including angiogenesis (14) and development (Binari, R. C., et al. Development, (Camb) 124, p. 2623-2632 (1997); Cumberledge and Reichsman, Trends Genet, 13, p. 421-423 (1997)). Heparinase I has been utilized in the sequence determination of sugars, in the preparation of small heparin fragments for therapeutic uses, and in the ex vivo removal of heparin from blood (Linhardt, R. J., Turnbull, J. E., Wang, H. M., Longanathan, D., & Gallagher, J. T. (1990) Biochemistry 29:2611-2617; Bernstein, H., Yang, V. C., Cooney, C. L., & Langer, R. (1988) Methods in Enzymol. 137:515-529). Extracorporeal medical devices (e.g. hemodialyzer pump-oxygenator) rely on systematic heparinization to provide blood compatibility within the device and a blood filter containing immobilized heparinase I at the effluent which is capable of neutralizing the heparin before the blood is returned to the body (Bernstein, H., Yang, V. C., Cooney, C. L., & Langer, R. (1988) Methods in Enzymol. 137:515-529).
There has been much speculation in the art about the possibility of creating “designer” enzymes, rationally designed to have desired substrate specificities and activities. Yet, although the importance of different levels (primary, secondary, and tertiary) of protein structure in determining the functional activity of enzymes has long been recognized, the lack of a broad and detailed understanding of the relationship between structure and function has prevented significant progress. Even for enzymes which have known activities, substrates, and primary structures, the general lack of information about secondary and tertuary structures and the relationship of these to function has made it difficult to predict the functional effect of any particular changes to the primary structure.